HEADER DNA BINDING PROTEIN 14-SEP-18 6MGM TITLE HELIX-LOOP-HELIX MOTIF OF MOUSE DNA-BINDING PROTEIN INHIBITOR ID-1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA-BINDING PROTEIN INHIBITOR ID-1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 52-104; COMPND 5 SYNONYM: INHIBITOR OF DNA BINDING 1,INHIBITOR OF DIFFERENTIATION 1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: ID1, ID, ID-1, IDB1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HELIX-LOOP-HELIX DNA-BINDING PROTEIN INHIBITOR, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.BENEZRA,N.P.PAVLETICH,Y.GOLDGUR,A.-L.GALL REVDAT 4 11-OCT-23 6MGM 1 REMARK REVDAT 3 04-DEC-19 6MGM 1 REMARK REVDAT 2 16-OCT-19 6MGM 1 JRNL REVDAT 1 18-SEP-19 6MGM 0 JRNL AUTH P.M.WOJNAROWICZ,R.LIMA E SILVA,M.OHNAKA,S.B.LEE,Y.CHIN, JRNL AUTH 2 A.KULUKIAN,S.H.CHANG,B.DESAI,M.GARCIA ESCOLANO,R.SHAH, JRNL AUTH 3 M.GARCIA-CAO,S.XU,R.KADAM,Y.GOLDGUR,M.A.MILLER,O.OUERFELLI, JRNL AUTH 4 G.YANG,T.ARAKAWA,S.K.ALBANESE,W.A.GARLAND,G.STOLLER, JRNL AUTH 5 J.CHAUDHARY,L.NORTON,R.K.SONI,J.PHILIP,R.C.HENDRICKSON, JRNL AUTH 6 A.IAVARONE,A.J.DANNENBERG,J.D.CHODERA,N.PAVLETICH, JRNL AUTH 7 A.LASORELLA,P.A.CAMPOCHIARO,R.BENEZRA JRNL TITL A SMALL-MOLECULE PAN-ID ANTAGONIST INHIBITS PATHOLOGIC JRNL TITL 2 OCULAR NEOVASCULARIZATION. JRNL REF CELL REP V. 29 62 2019 JRNL REFN ESSN 2211-1247 JRNL PMID 31577956 JRNL DOI 10.1016/J.CELREP.2019.08.073 REMARK 2 REMARK 2 RESOLUTION. 1.79 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10_2155 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.79 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.44 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 8775 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.640 REMARK 3 FREE R VALUE TEST SET COUNT : 934 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 21.4381 - 3.4229 0.99 1161 154 0.1728 0.2023 REMARK 3 2 3.4229 - 2.7186 1.00 1121 135 0.1824 0.2175 REMARK 3 3 2.7186 - 2.3755 1.00 1138 135 0.1755 0.2143 REMARK 3 4 2.3755 - 2.1585 1.00 1100 143 0.1641 0.2439 REMARK 3 5 2.1585 - 2.0039 0.99 1126 118 0.1738 0.2435 REMARK 3 6 2.0039 - 1.8858 0.99 1108 121 0.1981 0.2660 REMARK 3 7 1.8858 - 1.7914 0.97 1087 128 0.2138 0.2859 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.020 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 781 REMARK 3 ANGLE : 0.727 1055 REMARK 3 CHIRALITY : 0.048 126 REMARK 3 PLANARITY : 0.004 134 REMARK 3 DIHEDRAL : 15.878 493 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 1.7165 -0.6715 14.0714 REMARK 3 T TENSOR REMARK 3 T11: 0.1060 T22: 0.0980 REMARK 3 T33: 0.0902 T12: -0.0011 REMARK 3 T13: 0.0039 T23: 0.0063 REMARK 3 L TENSOR REMARK 3 L11: 1.7299 L22: 0.9257 REMARK 3 L33: 0.5527 L12: 0.0363 REMARK 3 L13: 0.2585 L23: 0.0822 REMARK 3 S TENSOR REMARK 3 S11: -0.0119 S12: 0.1676 S13: -0.0180 REMARK 3 S21: -0.1103 S22: 0.0309 S23: 0.0010 REMARK 3 S31: -0.0026 S32: -0.0006 S33: -0.0125 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6MGM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-SEP-18. REMARK 100 THE DEPOSITION ID IS D_1000236912. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-MAR-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X9A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.95 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8782 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 32.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.37600 REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 1MDY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CITRATE (PH 6.5), 0.2 M REMARK 280 MAGNESIUM ACETATE, 10% PEG8000, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 14.48950 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2090 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6310 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -26.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLU A 52 REMARK 465 GLN A 53 REMARK 465 GLN A 54 REMARK 465 VAL A 55 REMARK 465 ASN A 56 REMARK 465 VAL A 57 REMARK 465 LEU A 58 REMARK 465 LEU A 59 REMARK 465 TYR A 60 REMARK 465 GLU B 52 REMARK 465 GLN B 53 REMARK 465 GLN B 54 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH B 202 O HOH B 241 2.11 REMARK 500 ND2 ASN B 56 O HOH B 201 2.12 REMARK 500 O HOH B 203 O HOH B 223 2.14 REMARK 500 O HOH B 202 O HOH B 214 2.17 REMARK 500 O HOH A 209 O HOH A 237 2.17 REMARK 500 O HOH B 228 O HOH B 249 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 244 DISTANCE = 6.03 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5T9O RELATED DB: PDB DBREF 6MGM A 52 104 UNP P20067 ID1_MOUSE 52 104 DBREF 6MGM B 52 104 UNP P20067 ID1_MOUSE 52 104 SEQRES 1 A 53 GLU GLN GLN VAL ASN VAL LEU LEU TYR ASP MET ASN GLY SEQRES 2 A 53 CYS TYR SER ARG LEU LYS GLU LEU VAL PRO THR LEU PRO SEQRES 3 A 53 GLN ASN ARG LYS VAL SER LYS VAL GLU ILE LEU GLN HIS SEQRES 4 A 53 VAL ILE ASP TYR ILE ARG ASP LEU GLN LEU GLU LEU ASN SEQRES 5 A 53 SER SEQRES 1 B 53 GLU GLN GLN VAL ASN VAL LEU LEU TYR ASP MET ASN GLY SEQRES 2 B 53 CYS TYR SER ARG LEU LYS GLU LEU VAL PRO THR LEU PRO SEQRES 3 B 53 GLN ASN ARG LYS VAL SER LYS VAL GLU ILE LEU GLN HIS SEQRES 4 B 53 VAL ILE ASP TYR ILE ARG ASP LEU GLN LEU GLU LEU ASN SEQRES 5 B 53 SER FORMUL 3 HOH *95(H2 O) HELIX 1 AA1 ASP A 61 VAL A 73 1 13 HELIX 2 AA2 SER A 83 ASN A 103 1 21 HELIX 3 AA3 ASP B 61 VAL B 73 1 13 HELIX 4 AA4 SER B 83 GLU B 101 1 19 CRYST1 32.165 28.979 50.333 90.00 97.94 90.00 P 1 21 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.031090 0.000000 0.004336 0.00000 SCALE2 0.000000 0.034508 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020060 0.00000